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- PDB-3qek: Crystal structure of amino terminal domain of the NMDA receptor s... -

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Basic information

Entry
Database: PDB / ID: 3qek
TitleCrystal structure of amino terminal domain of the NMDA receptor subunit GluN1
ComponentsNMDA glutamate receptor subunit
KeywordsTRANSPORT PROTEIN / amino terminal domain / ion channel / NMDA receptor / allosteric modulation / phenylethanolamine / polyamine / extracellular / membrane
Function / homology
Function and homology information


NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to zinc ion / regulation of membrane potential / chemical synaptic transmission / postsynaptic membrane / neuron projection / metal ion binding / plasma membrane
Similarity search - Function
: / : / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain ...: / : / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsKarakas, E. / Simorowski, N. / Furukawa, H.
CitationJournal: Nature / Year: 2011
Title: Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors.
Authors: Karakas, E. / Simorowski, N. / Furukawa, H.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NMDA glutamate receptor subunit
B: NMDA glutamate receptor subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4329
Polymers86,8822
Non-polymers1,5507
Water5,909328
1
A: NMDA glutamate receptor subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5095
Polymers43,4411
Non-polymers1,0684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NMDA glutamate receptor subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9234
Polymers43,4411
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint6 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.323, 92.813, 209.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NMDA glutamate receptor subunit


Mass: 43441.188 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain, residues 23-405 / Mutation: N61Q, N371Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 150mM KNO3, 50mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2009
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 120092 / Num. obs: 120092 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.396 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2-2.070.3964.3120591100
2.07-2.150.2676.7120121100
2.15-2.250.2029.3120431100
2.25-2.370.15213119631100
2.37-2.520.11417.5119921100
2.52-2.710.08521.6119601100
2.71-2.990.06425.8120781100
2.99-3.420.05230.6119791100
3.42-4.310.05529.4120581100
4.31-500.03937.611948199.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.001→29.948 Å / SU ML: 0.26 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 5995 5.12 %RANDOM
Rwork0.192 ---
all0.1938 120092 --
obs0.1938 117186 97.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.749 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.4493 Å20 Å2-0 Å2
2--0.7207 Å2-0 Å2
3----7.1701 Å2
Refinement stepCycle: LAST / Resolution: 2.001→29.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 97 328 5983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095793
X-RAY DIFFRACTIONf_angle_d1.0647848
X-RAY DIFFRACTIONf_dihedral_angle_d13.5242134
X-RAY DIFFRACTIONf_chiral_restr0.07910
X-RAY DIFFRACTIONf_plane_restr0.005990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.02350.23871700.22373111X-RAY DIFFRACTION83
2.0235-2.04740.30261930.23443555X-RAY DIFFRACTION91
2.0474-2.07230.28961880.2213516X-RAY DIFFRACTION93
2.0723-2.09850.28611930.2293543X-RAY DIFFRACTION94
2.0985-2.12610.29171860.21853713X-RAY DIFFRACTION95
2.1261-2.15530.26831870.20023621X-RAY DIFFRACTION95
2.1553-2.1860.23752190.19923559X-RAY DIFFRACTION96
2.186-2.21870.26271920.19343688X-RAY DIFFRACTION96
2.2187-2.25330.28781840.20413754X-RAY DIFFRACTION96
2.2533-2.29030.22662040.19713607X-RAY DIFFRACTION97
2.2903-2.32970.27471520.20223770X-RAY DIFFRACTION97
2.3297-2.37210.2332330.19463733X-RAY DIFFRACTION97
2.3721-2.41770.27211810.18883704X-RAY DIFFRACTION98
2.4177-2.4670.21821970.20093747X-RAY DIFFRACTION98
2.467-2.52060.24231620.20593749X-RAY DIFFRACTION98
2.5206-2.57920.2512150.20223752X-RAY DIFFRACTION99
2.5792-2.64370.26422060.19853801X-RAY DIFFRACTION98
2.6437-2.71510.2642080.20993734X-RAY DIFFRACTION99
2.7151-2.7950.26361720.21363863X-RAY DIFFRACTION99
2.795-2.88510.23412070.20613775X-RAY DIFFRACTION99
2.8851-2.98810.25472300.21273784X-RAY DIFFRACTION99
2.9881-3.10770.27472160.20853754X-RAY DIFFRACTION99
3.1077-3.24890.22492210.20093795X-RAY DIFFRACTION100
3.2489-3.420.23152260.19713797X-RAY DIFFRACTION100
3.42-3.63390.21231810.1843841X-RAY DIFFRACTION100
3.6339-3.91390.19612140.17683803X-RAY DIFFRACTION100
3.9139-4.30680.18542490.1623764X-RAY DIFFRACTION100
4.3068-4.92760.18232160.15193767X-RAY DIFFRACTION100
4.9276-6.19920.23331710.20173865X-RAY DIFFRACTION100
6.1992-29.95090.19462220.19083726X-RAY DIFFRACTION98

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